Scientists fear that doctors are overprescribing an antibiotic linked to nerve damage and tendon ruptures that have caused permanent disability.
They want tighter restrictions on fluoroquinolones, which are also becoming less effective on the bacterium that causes gonorrhoea as it grows more resistant to the drug.
Fluoroquinolones can be used to kill a wide range of bacteria and are often prescribed for severe urinary tract infections or acute bacterial infections of the prostate.
GPs in New Zealand are allowed to prescribe a type known as Ciprofloxacin but because of the potential side effects, microbiologists are calling for more restrictions.
Pharmac has a list of approved conditions they should be used for, and the Ministry of Health advises that in most cases, they should only be used once other antibiotics haven't worked.
But documents released to the Herald from each of the country's 20 District Health Boards under the Official Information Act have revealed:
• 2013/2014 audits of several hospitals' use found in many cases - up to 40 per cent in some - fluoroquinolones were given to people suffering from illnesses other than those specified by Pharmac.
• Only 42 per cent of the 19 patients at Whanganui DHB prescribed Ciprofloxacin in August 2014 had been given it for an approved use.
• The New Zealand Centre for Adverse Reaction Monitoring (CARM) has received 445 reports of suspected negative reactions to fluoroquinolones since 2007. That included 64 cases of tendinitis and 24 tendon ruptures.
• The drug was dispensed from community pharmacies across the country more than 1.8 million times in the last decade.
• Prescriptions for fluoroquinolone eye drops - recommended for an infection of the cornea and sometimes used to treat middle ear infections- have increased by more than 300 per cent.
Clinical director of infection services at Middlemore, Dr David Holland, and Eamon Duffy, the pharmacist in charge of improving the use of antibiotics at Auckland District Health Board wrote a letter to Pharmac - which allocates the funding for drugs - on May 8 last year recommending the regulator further restrict funding of Ciprofloxacin.
They want it under a "special authority" classification which would require GPs to get approval from an infectious disease specialist or microbiologist before prescribing it.
Ciprofloxacin increased in use to become the 10th most heavily used antibiotic in New Zealand between 2006 and 2014, and during this period resistance to the drug had increased, including in the bacterium which causes gonorrhoea, the letter said.
Australia had heavily restricted the use of fluoroquinolones by changing how it was funded and had lower rates of use and resistance than New Zealand, the letter said.
But Pharmac have not announced any plans to further restrict the drugs and in October instead widened the criteria for Ciprofloxacin eye drops, allowing them to be used to treat middle ear infections.
Sarah Fitt, Pharmac's director of operations, told the Herald the organisation sought advice from the Pharmacology and Therapeutics Advisory Committee on how medicine should be used.
And although most of the responsibility for prescribing medications sat with medical practitioners, it worked with other authorities like the Best Practice Advocacy Centre (BPACnz) and Auckland University's Goodfellow Unit to provide doctors with guidance.
In 2013, in a newsletter update for his pathology service, clinical microbiologist Dr Michael Addidle warned doctors in the Bay of Plenty of the increasing use of fluoroquinolones in the area and rise in resistance of urinary E.coli to the drugs.
He said GPs should only prescribe ciprofloxacin for gonorrhoea that was resistant to other antibiotics, confirmed cases of Pseudomonas spp (a bacteria that can cause UTIs), kidney infections or prostatitis.
"All other clinical indications should be discussed with a clinical microbiologist or infectious disease specialist before prescribing ciprofloxacin," Addidle wrote.
In 2016, Rotorua Hospital's pharmacy removed another kind of fluoroquinolone, Norfloxacin, from shelves after a local microbiologist raised concerns about how it was being prescribed. It can now only be ordered after approval from an infectious disease specialist.
The Ministry of Health said it was investigating how to develop a system for monitoring the prescription of antibiotics - including fluoroquinolones - as part of its New Zealand Antimicrobial Resistance Action Plan.
Guidelines from BPACnz - an independent non-profit for the education of medical practitioners in New Zealand - used by the Ministry of Health state Ciprofloxacin can be used against severe or prolonged campylobacter food poisoning, gonorrhoea, mild kidney infections in adults and skin infections in the ear known as otitis externa with secondary infection. However this should occur only once other antibiotics have been tried first and haven't worked.
It should only ever be used first, instead of other treatments, for severe salmonella food poisoning or for some kinds of UTIs.
A spokesman for Medsafe said the number of negative reactions were "in line with what is expected from the data sheets for the individual medicines".
It continuously monitored the safety of all medicines and was confident the benefits fluoroquinolones outweighed the risks of harm when used appropriately.
In September, Richard Pyne, from Glasgow, told Al Jazeera that he had not been able to walk in more than a year after taking Ciprofloxacin for prostatitis.
Essex woman Jane Allan said in a Daily Mail report in 2016 that symptoms including tingling and burning sensations lasted months after she stopped taking the drug.
The US Food and Drug Administration has repeatedly warned about the "disabling and potentially permanent serious side effects" of fluoroquinolones taken orally.
They can affect the nervous system, tendons, muscles and joints and include tendon ruptures and peripheral neuropathy (nerve damage to the arms and legs).
In a drug safety communication issued in 2016, the agency said the risk generally outweighed the benefits of using fluoroquinolones to treat many illnesses - including acute sinusitis and uncomplicated urinary tract infections (UTIs).